Update actions infra, pin zarr

tskit-dev · Jul 10, 2024 · 8d5d4c4 · 8d5d4c4
1 parent 2edadb6
commit 8d5d4c4
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Showing 14 changed files with 127 additions and 102 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -26,8 +26,6 @@ jobs:
       - run:
           name: Run Python tests 
           command: |
-            # Run setup.py so that the version is defined
-            python3 setup.py build
             python3 -m pytest --cov=tszip --cov-report=xml --cov-branch -n 2 tests
             codecov
             rm .coverage
@@ -40,13 +38,10 @@ jobs:
           name: Build Python package
           command: |
             rm -fR build
-            python setup.py sdist
-            python setup.py check
-            python -m twine check dist/*.tar.gz
             python -m venv venv
             source venv/bin/activate 
-            pip install --upgrade setuptools pip wheel
-            python setup.py build_ext
-            python setup.py egg_info
-            python setup.py bdist_wheel
+            pip install --upgrade setuptools pip wheel build twine
+            python -m build --sdist
+            python -m twine check dist/*.tar.gz
+            python -m build --wheel
             pip install dist/*.tar.gz 
diff --git a/.github/workflows/docker/buildwheel.sh b/.github/workflows/docker/buildwheel.sh
@@ -11,7 +11,7 @@ echo "arch=$ARCH"
 for V in "${PYTHON_VERSIONS[@]}"; do
     PYBIN=/opt/python/$V/bin
     rm -rf build/       # Avoid lib build by narrow Python is used by wide python
-    $PYBIN/python setup.py bdist_wheel
+    $PYBIN/python -m build --wheel
 done
 
 rm dist/*.tar.gz
diff --git a/.github/workflows/docker/shared.env b/.github/workflows/docker/shared.env
@@ -1,6 +1,6 @@
 PYTHON_VERSIONS=(
+    cp312-cp312
     cp311-cp311
     cp310-cp310
     cp39-cp39
-    cp38-cp38
 )
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -13,13 +13,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.11.0
+        uses: styfle/cancel-workflow-action@0.12.1
         with:
           access_token: ${{ github.token }}
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.10"
           cache: 'pip'

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -11,80 +11,48 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.12.0
+        uses: styfle/cancel-workflow-action@0.12.1
         with:
           access_token: ${{ github.token }}
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
       - uses: pre-commit/action@v3.0.0
 
   test:
     name: Python
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python: [ 3.8, 3.11 ]
+        python: [ 3.9, 3.12 ]
         os:  [ macos-latest, ubuntu-latest, windows-latest ]
     defaults:
       run:
         shell: bash
     steps:
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.6.0
+        uses: styfle/cancel-workflow-action@0.12.1
         with:
           access_token: ${{ github.token }}
 
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           submodules: true
 
-      - name: Cache conda and dependancies
-        id: cache
-        uses: actions/cache@v2
-        with:
-          path: |
-            c:\Miniconda\envs\anaconda-client-env
-            /usr/share/miniconda/envs/anaconda-client-env
-            ~/osx-conda
-            ~/.profile
-          key: ${{ runner.os }}-${{ matrix.python}}-conda-v10-${{ hashFiles('requirements/CI-tests-conda.txt') }}
-
       - name: Install Conda
-        uses: conda-incubator/setup-miniconda@v2
-        if: steps.cache.outputs.cache-hit != 'true'
+        uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: anaconda-client-env
           python-version: ${{ matrix.python }}
           channels: conda-forge
           channel-priority: strict
           auto-update-conda: true
 
-      - name: Fix windows .profile
-        if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'windows-latest'
-        run: |
-          cp ~/.bash_profile ~/.profile
-
       - name: Install conda deps
-        if: steps.cache.outputs.cache-hit != 'true'
         shell: bash -l {0} #We need a login shell to get conda
         run: |
-          conda install mamba
-          mamba install --yes --file=requirements/CI-tests-conda.txt
-
-      - name: Fix OSX Cache Write #OSX Won't let the cache restore due to file perms
-        if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'macos-latest'
-        run: |
-          cp -r /usr/local/miniconda/envs/anaconda-client-env ~/osx-conda
-
-      - name: Fix OSX Cache Restore
-        if: steps.cache.outputs.cache-hit == 'true' && matrix.os == 'macos-latest'
-        run: |
-          mkdir -p /usr/local/miniconda/envs
-          sudo cp -r ~/osx-conda /usr/local/miniconda/envs/anaconda-client-env
+          conda install --yes --file=requirements/CI-tests-conda.txt
 
       - name: Run tests
         run: |
-          source ~/.profile
-          conda activate anaconda-client-env
           python -m pytest -xv -n2
diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
@@ -15,22 +15,22 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
             submodules: true
 
       - name: Set up Python 3.10
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: "3.10"
 
       - name: Build sdist
         shell: bash
         run: |
-          python setup.py sdist
+          python -m build --sdist
 
       - name: Upload sdist
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: sdist
           path: dist
@@ -41,7 +41,7 @@ jobs:
           docker run --rm -v `pwd`:/project -w /project quay.io/pypa/manylinux2014_x86_64 bash .github/workflows/docker/buildwheel.sh
 
       - name: Upload Wheels
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: wheels
           path: dist
@@ -51,14 +51,14 @@ jobs:
     runs-on: macos-latest
     strategy:
       matrix:
-        python: [3.8, 3.8, 3.9, "3.10", "3.11"]
+        python: [3.9, "3.10", 3.11, 3.12]
     steps:
       - name: Download wheels
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v4
         with:
           name: wheels
       - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
       - name: Install wheel and test
@@ -73,15 +73,15 @@ jobs:
     runs-on: windows-latest
     strategy:
       matrix:
-        python: [3.8, 3.8, 3.9, "3.10", "3.11"]
+        python: [3.9, "3.10", 3.11, 3.12]
         wordsize: [64]
     steps:
       - name: Download wheels
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v4
         with:
           name: wheels
       - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
       - name: Install wheel and test
@@ -97,14 +97,14 @@ jobs:
     needs: ['manylinux']
     strategy:
       matrix:
-        python: [3.8, 3.8, 3.9, "3.10", "3.11"]
+        python: [3.9, "3.10", 3.11, 3.12]
     steps:
       - name: Download wheels
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v4
         with:
           name: wheels
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
       - name: Install wheel and test
@@ -123,7 +123,7 @@ jobs:
       id-token: write
     steps:
       - name: Download all
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v4
       - name: Move to dist
         run: |
           mkdir dist

diff --git a/.mergify.yml b/.mergify.yml
@@ -4,12 +4,12 @@ queue_rules:
       - "#approved-reviews-by>=1"
       - "#changes-requested-reviews-by=0"
       - status-success=Lint
-      - status-success=Python (3.8, macos-latest)
-      - status-success=Python (3.11, macos-latest)
-      - status-success=Python (3.8, ubuntu-latest)
-      - status-success=Python (3.11, ubuntu-latest)
-      - status-success=Python (3.8, windows-latest)
-      - status-success=Python (3.11, windows-latest)
+      - status-success=Python (3.9, macos-latest)
+      - status-success=Python (3.12, macos-latest)
+      - status-success=Python (3.9, ubuntu-latest)
+      - status-success=Python (3.12, ubuntu-latest)
+      - status-success=Python (3.9, windows-latest)
+      - status-success=Python (3.12, windows-latest)
       - "status-success=ci/circleci: build"
 pull_request_rules:
   - name: Automatic rebase, CI and merge
@@ -20,12 +20,12 @@ pull_request_rules:
       - base=main
       - label=AUTOMERGE-REQUESTED
       - status-success=Lint
-      - status-success=Python (3.8, macos-latest)
-      - status-success=Python (3.11, macos-latest)
-      - status-success=Python (3.8, ubuntu-latest)
-      - status-success=Python (3.11, ubuntu-latest)
-      - status-success=Python (3.8, windows-latest)
-      - status-success=Python (3.11, windows-latest)
+      - status-success=Python (3.9, macos-latest)
+      - status-success=Python (3.12, macos-latest)
+      - status-success=Python (3.9, ubuntu-latest)
+      - status-success=Python (3.12, ubuntu-latest)
+      - status-success=Python (3.9, windows-latest)
+      - status-success=Python (3.12, windows-latest)
       - "status-success=ci/circleci: build"
     actions:
       queue:

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,3 +1,9 @@
+--------------------
+[0.2.4] - 2024-01-XX
+--------------------
+
+- tszip now supports Python 3.12, 3.8 support has been removed.
+
 --------------------
 [0.2.3] - 2023-10-30
 --------------------

diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,62 @@
+[build-system]
+requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "tszip"
+authors = [
+    {name = "Tskit Developers", email = "admin@tskit.dev"},
+]
+description = "Compression utilities for tree sequences"
+readme = "README.md"
+requires-python = ">=3.8"
+license = {text = "MIT"}
+classifiers = [
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3 :: Only",
+    "Development Status :: 5 - Production/Stable",
+    "Environment :: Other Environment",
+    "Intended Audience :: Science/Research",
+    "Operating System :: POSIX",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: Microsoft :: Windows",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "License :: OSI Approved :: MIT License",
+]
+keywords = ["tree sequence", "tskit"]
+dependencies = [
+    "numpy",
+    "humanize",
+    "tskit>=0.3.3",
+    "numcodecs>=0.6.4",
+    "zarr<3",
+]
+dynamic = ["version"]
+
+[project.urls]
+Homepage = "http://pypi.python.org/pypi/tszip"
+Documentation = "https://tszip.readthedocs.io/en/latest/"
+Changelog = "https://tszip.readthedocs.io/en/latest/changelog.html"
+"Bug Tracker" = "https://github.com/tskit-dev/tszip/issues"
+GitHub = "https://github.com/tskit-dev/tszip/"
+
+[project.scripts]
+tszip = "tszip.cli:tszip_main"
+tsunzip = "tszip.cli:tsunzip_main"
+
+[tool.setuptools]
+packages = ["tszip"]
+include-package-data = true
+
+[tool.setuptools_scm]
+write_to = "tszip/_version.py"
+
+[tool.pytest.ini_options]
+addopts = "-n 4"
+testpaths = ["tests"]
diff --git a/requirements/CI-docs.txt b/requirements/CI-docs.txt
@@ -1,8 +1,8 @@
-humanize==4.8.0
-jupyter-book==0.15.1
+humanize==4.10.0
+jupyter-book==1.0.2
 numcodecs==0.12.1
-sphinx-issues==3.0.1
+sphinx-issues==4.1.0
 sphinx-argparse==0.4.0
-setuptools_scm==8.0.4
-tskit==0.5.6
-zarr==2.16.1
+setuptools_scm==8.1.0
+tskit==0.5.8
+zarr==2.18.2
diff --git a/requirements/CI-tests-conda.txt b/requirements/CI-tests-conda.txt
@@ -1,8 +1,8 @@
-humanize==4.8.0
-h5py==3.7.0
-msprime==1.2.0
-pytest==7.4.2
-pytest-cov==4.1.0
-pytest-xdist==3.3.1
-tskit==0.5.6
-zarr==2.16.1
+humanize==4.10.0
+h5py==3.11.0
+msprime==1.3.2
+pytest==8.2.2
+pytest-cov==5.0.0
+pytest-xdist==3.6.1
+tskit==0.5.8
+zarr==2.18.2